FONZIE Files

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							WELCOME TO THE README FILE OF FONZIE
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INTRODUCTION
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This file helps you to understand how to run the FONZIE pipeline.

FONZIE is an informatics tool developed for the genetic cartography speciality.
In this way, FONZIE allow as well to find markers on a set of sequences than to find
associate oligonucleotides.

FONZIE calls Tandem Repeat Finder (TRF) on the input nucleic sequence(s) 
file (FASTA format).
Each marker is screened regarding different criteria (size, percent of 
matches, presence in specific regions of the input sequence).
Then, marker's sensitivity is established by performing a BLAST against 
a database of nucleic sequences (which include the input file)
This database has to be created before the use of FONZIE.
In the next step, primer pairs are designed, using Primer3, for the 
selected markers.
FONZIE then test the sensitivity of the amplification product using 
BLAST against the database.
The output files of FONZIE are a tab-delimited text file including data 
on markers and primers, a dat file which is the output
of TRF and 3 directories containing respectively, the marker sequence 
in FASTA, the amplification product sequence in FASTA
and a data file for each marker.


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REQUIREMENTS
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What do you need to run FONZIE ?

- Python: the language the pipeline is primarily written
	[http://www.python.org/download/]

- Tandem Repeat Finder: to identify tandem repeat
	WARNING: the executable has to be rename "trf.exe"
	[http://tandem.bu.edu/trf/trf.download.html]

- Blastall: to perform blast steps
- Formatdb: to create a database
	[ftp://ftp.ncbi.nih.gov/blast/]

- Primer3_core: to design primers
	[http://primer3.sourceforge.net/releases.php]

and of course, all the files in the FONZIE package.


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INSTALLATION
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To run FONZIE, make sure the required softwares are installed on your computer and their 
location are within your $PATH.

Be sure that the executable of Tandem Repeat Finder is rename "trf"

Add the directory containing FONZIE files in your $PATH and make sure the scripts
xFonzie.py and Fonzie.py are executable.


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RUNNING FONZIE WITH GRAPHIC USER INTERFACE
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1. Create a database using formatdb.
	[formatdb -i <file name> -pF -oT -n <database name>]
	WARNING: blastall WON'T work if there are any spaces in the database pathway

2. Run the xFonzie.py script
	[./xFonzie.py]

3. Load the sequence (fasta or multifasta)

4. Load the database

5. GO FONZIE!!

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RUNNING FONZIE WITHOUT GRAPHIC USER INTERFACE
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1. Create a database using formatdb.
	[formatdb -i <file name> -pF -oT -n <database name>]
	WARNING: blastall WON'T work if there are any spaces in the database pathway

2. Write the parameters of TRF, BLAST, the screening ,the database pathway and Primer3 
	in a file (e.g. "parameters.txt"), as explain in the template file "parameters_template.txt"
	(include in the package and always in the directory containing FONZIE files)

3. Run the Fonzie.py script on the sequence (fasta or multifasta)
	[./Fonzie.py -i sequence.fasta -p parameters.txt]
	
	the "-h" option will remind you the usage of FONZIE.


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OUTPUTS
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All outputs are displayed in a new directory (named after the sequence) in the query 
sequence directory.

3 directories are created:
- MARKERS_SEQUENCES: contains the sequence (fasta) of each marker generated
- AMPLIF_PRODUCTS_SEQUENCES: contains the sequence (fasta) of each amplification product
- MARKERS_RECAP: contains a recapitulative informations file for each marker generated

3 files are created:
- a .dat file, which is the output of TRF
- a tab delimited text file containing the outputs of TRF and the screening step
- a tab delimited text file containing the results of FONZIE


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BUGS ?
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Yes, there can be bugs in this software.

Make sure to read this file carefully...

If the problems remain, you can contact us at:
	
	jonathan.grandaubert@versailles.inra.fr
	pascal.bally@versailles.inra.fr


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COPYRIGHT
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Copyright (C) 2010 - Jonathan Grandaubert & Pascal Bally

FONZIE is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
###
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.